Most labs in Canada not fully able to detect Delta COVID-19 variant, experts warn
Canada’s current efforts to identify COVID-19 variants, especially that of Delta B.1.617, may not be enough to truly track its spread across the country, according to several experts.
According to Dr. Laurence Pelletier, a researcher from the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, public health units across the provinces are, for the most part, not equipped with testing equipment that can fully sequence or identify some COVID-19 variants.
One such variant of concern is that of the Delta B.1.617, which was first discovered in India. Speaking with Global News Friday, both Pelletier and Mount Sinai co-researcher Dr. Jeff Wrana said that the number of mutations in the Delta variant made it very difficult for tests to properly identify it.
According to them, a majority of public health labs are using “more conventional” PCR tests that are limited due to them being only able to look at one or two specific mutations. While those tests work well for variants of concern like the Alpha B.1.1.7, those with three or more mutations like the Delta variant can’t be distinguished.
“The obvious answer to that is no, there’s not enough variant testing across Canada and there’s not even enough in Ontario, to be honest,” said Pelletier, who worked alongside Wrana and Mount Sinai’s Dr. Tony Mazzulli to screen over 11,000 positive cases from all across the Greater Toronto Area.
Pelletier said that daily reports from Public Health Ontario saw the frequency of the Alpha variant decreasing, which he suggests as an indication of other variants of concern, like Delta, expanding. Though, because of the difficulties in identifying variants with more mutations, public health units like the ones in Ontario and many other provinces are having difficulty in pinpointing which exact ones were spreading.
With the use of a new testing method that uses a robot and sequencing platform called SPAR-seq, Pelletier and Wrana revealed that Delta had accounted for about 20 per cent of new positive cases just based on their data, with the possibility of that number being much higher.
Pelletier and Wrana, who were part of the lab that identified the first Delta variant in Ontario, said that their sequencing method could be done much faster and at a fraction of the cost than other labs.
In a press conference Friday, Global News had asked Canada’s Chief Public Health Officer Dr. Theresa Tam if enough sequencing was being done to identify the Delta variant. In response, Tam said that Canada as a country was doing “a lot more sequencing than many,” as its number of cases continues to decrease.
“The provinces are, in fact, moving towards sequencing a vast majority of positive cases,” she said.
Tam also pointed at increasing evidence of Delta being more transmissible than the Alpha variant and cited a recent study from the United Kingdom that suggests two vaccine doses to be much more effective in protecting against it.
“As supplies increase … it is very important to get a second dose when variants such as the Delta variant is in our community,” she said.
When asked by Global News on Saturday as to the exact extent of public health units’ difficulties in identifying Delta, Health Canada referred to Tam’s comments from Friday.
Out of the four variants of concern listed on Health Canada’s COVID-19 epidemiology website, the only variant that has no numbers accounted for or tracked to the same extent is Delta B.1.617. Health Canada did not answer Global News’ questions as to why the variant wasn’t being counted yet, though according to the website, it is “still being assessed” after having been identified in all ten provinces and one territory.
According to Dr. Gerald A. Evans, the chair of infectious diseases at Queen’s University, the Delta variant’s lack of the N501Y mutation and inclusion of E484Q and L452R mutations made it harder for labs to screen.
“So [yes], it is a little bit harder to spot, there’s no question about it,” said Evans. “We can’t rely on the very rapid sort of PCR test that we had looking at Alpha, Beta and Gamma because they have N501Y mutation.”
While Evans agreed that there were obstacles in determining how far the virus had truly spread across the country, he pointed that the uncertainty from a lack of data could be a positive.
“So this is the problem we’re at right now — you’re either a glass half-full person or a glass half-empty person,” he said, noting that Canada’s dwindling new case numbers probably meant that the true spread of the virus would be actually quite small.
According to him, if that variant was accounted for a sizeable amount of new cases when Canada’s third wave was in full swing, he would be worried. Though today, with just a fraction of cases compared to our peak, Evans said that the country was in a much different stage of the pandemic now given the ramped-up vaccine rollout and stringent public health measures.
“And I’ll tell you that I consider myself a pessimist, but I’m actually not that pessimistic about this because I think we’re in a very different phase of the pandemic,” he said.globalnews